There does exist animated footage that was not used in the movie.
During the early stages of production, some animation was
produced in an attempt to assemble a rough "trade trailer" that could be used
to shop the film around to potential distributors. This trailer was never releaed in theaters.
While much of the footage did end up being used in the final cut of the movie, a lot of it did not.
Such 'lost footage' includes additional shots of Unicron eating
Lithone, a completely white Autobot City with a differently colored
Ultra Magnus (which are actually his original Diaclone toy colors),
a completely different version of the scene in which Kup
tells the Dinobots about the "gigantic igyak," and the Unicron
transformation sequence which is about the same as the final cut except
for the editing and one shot with Galvatron falling. (Since this
sequence was filmed much earlier than the later shots involving Unicron,
Unicron's head is drawn differently in later scenes than in this one,
as is the Matrix.)
The entire 'trade trailer' is about 3-4 minutes long.

The original script includes scenes not found in the final
version of the movie. Those interested in owning it may order a bound copy from
Script City at: 8033 Sunset Blvd., Ste.1500, Hollywood, CA 90046,
Phone: 1-800-676-2522. I suggest calling for prices.

As Sludge is being beaten by Devastator, you can see his eyeballs
popping out and then going back in. (see image) The animators probably
put this in as a cartoon gag.

The movie was written in 1984, early in the development of the TV
series. Therefore, many of the characters who were introduced later in
the TV series but before the movie chronologically (like the Aerialbots,
the Stunticons, the Combaticons, etc.) do not appear because they did
not exist at the time the script was written.

In the original PG-rated theatrical release of the film, Spike says:
"Oh shit, what are we gonna do now?" just before being sucked into Unicron.
The negative response to this interjection caused the studio to release
an unrated edited version for video, with this line cut down to just
"What are we gonna do now?" In both versions, however, Ultra Magnus
says, "Open, dammit, open!" while trying to open the Matrix. (Update:
This line can be heard in the recently re-released version from Malofilm.)

Originally, the characters of Steeljaw, Ramhorn, Rewind, and Eject were to
called "Cubbie" (lion), "Stripes" (tiger), "Stinger" (scorpion), and "Bolts" (robot).

The opening titles (with the computerized tunnel sequence) were
designed by Deena Burkett and Bill Millar. Deena Burkett had worked
previously as visual effects scene co-ordinator for Disney's Tron.

For those who wish that Reflector had made an appearance in the movie,
it should be noted that one of the three Reflector robots DOES appear,
if only briefly. In the battle at Autobot City, there is a shot where
the Decepticons regroup, just before the Constructicons form Devastator,
and just before Springer says: "Come on, Arcee! We've got to get this
launcher into place!" Reflector can be seen as one of the last ones
in the armada, right in front of Dirge.

Habsro attempted to make an Arcee toy back in 1986, but this toy
never made it past the prototype stage. Years later there was an Arcee model kit (in robot mode) released
in Japan by the company MC Axis.

The character of Arcee had her first officially licensed toy in the form of the BotCon 2001
exclusive repaint of Transmetal Blackarachnia. (See photos at the BotCon 2001 Merchandise page.)
Later, there was a small Arcee PVC figure, released in the U.S. as part of the "Heroes of Cybertron" line.

The Transformers: Energon toyline now includes a pink motorcycle figure named Arcee that pays homage to the
original character, yet has many differences. Ben Yee
has pics and a review of this toy at BWTF.com.

Likewise, there were no toys for the Quintessons, the Lithonians, nor any of the Junkions other than Wreck-Gar. The toy for the Sharkticon was sold as a Decepticon named Gnaw.

There WAS at least one prototype made for a 1986 Unicron figure, but it was never released as a toy. See the pictures at the Toys page.
Hasbro finally released a Unicron toy in 2003 as part of their Transformers: Armada toy line.